[1][IUCr Home Page] [2][CIF Home Page] [3][ciftbx.src] [4][cyclops.src]
   [5][cif2cif.src] [6][cif2xml.src] [7][cif2pdb.src]
     __________________________________________________________________

     CIFtbx, Cyclops, cif2cif, cif2xml, cif2pdb README FIRST Information

                  CIFtbx Version 4.1.1 Release, March 2024
          Copyright © 2024 Sydney R. Hall and Herbert J. Bernstein
                    Cyclops Version 2.1.5, November 2009
          Copyright © 2009 Sydney R. Hall and Herbert J. Bernstein
                     cif2cif Version 2.0.1, January 2024
    Copyright © 1997, 1998, 2000, 2005, 2009, 2024 Herbert J. Bernstein
                  cif2xml Version 0.1.1 beta, November 2009
                Copyright © 2000, 2009 Herbert J. Bernstein
                    cif2pdb Version 2.0.3, November 2009
      Copyright © 2000, 2005, 2009 Herbert J. Bernstein and Frances C.
                                  Bernstein

                               Sydney R. Hall
   Crystallography Centre, University of Western Australia, Nedlands 6009,
                                  Australia
            Phone: +61 9 380 2725, e-mail: syd@crystal.uwa.edu.au

                            Herbert J. Bernstein
       Bernstein+Sons, 11 Riverside Drive, Apt 5UE, NY 10023-1317, USA
            Phone: 1-212-877-1686, e-mail: yayahjb@gmail.com.com

                            Frances C. Bernstein
       Bernstein+Sons, 11 Riverside Drive, Apt 5UE, NY 10023-1317, USA
         Phone: 1-212-877-1686, e-mail: fcb@bernstein-plus-sons.com
     __________________________________________________________________

   YOU MAY REDISTRIBUTE THE CBFLIB PACKAGE UNDER THE TERMS OF THE [8]GPL.

   ALTERNATIVELY YOU MAY REDISTRIBUTE THE CBFLIB API UNDER THE TERMS OF
   THE [9]LGPL.
     __________________________________________________________________

   Work on these programs has been supported by grants from various
   government agencies and the IUCr. See the documentation of the
   individual programs for further information.

   CIFtbx4, Cyclops, cif2cif, cif2xml and cif2pdb are free software; you
   can redistribute this software and/or modify this software under the
   terms of the GNU General Public License as published by the Free
   Software Foundation; either version 2 of the License, or (at your
   option) any later version.

   Alternatively you may reditribute and/or modify the CIFtbx API (but not
   the programs) under the terms of the GNU Lesser General Public License
   as published by the Free Software Foundation; either version 2.1 of the
   License, or (at your option) any later version.

   This software is distributed in the hope that it will be useful, but
   WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
   General Public License for more details.

   You should have received a copy of the GNU General Public License along
   with this software; if not, write to the Free Software Foundation,
   Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

   You should have received a copy of the GNU Lesser General Public
   License along with this software; if not, write to the Free Software
   Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

                 Before using this software, please read the
                                 [10]NOTICE
                          and please read the IUCr
                                 [11]Policy
          on the Use of the Crystallographic Information File (CIF)
     __________________________________________________________________

   CIFtbx is a tool box of Fortran routines for manipulating CIF data.
   CYCLOPS2, cif2cif, cif2xml and cif2pdb are open source Fortran programs
   based on CIFtbx. CYCLOPS2 checks STAR data names against data name
   dictionaries. cif2cif copies a CIF to a CIF while checking data names
   against dictionaries and reformating numbers with esd's to conform to
   the rule of 19. A request list may be specified. cif2xml is a variant
   of cif2cif which produces XML output. cif2pdb converts mmCIF files to a
   PDB or WPDB format.

   In order to ensure continuing availability of source code and
   documentation most programs and documents on this site are subject to
   copyright. This does not prevent you from using the programs, from
   making copies and changes, but prevents the creation of "closed source"
   versions out of the open source versions. See [12]NOTICE.

   Science is best served when the tools we use are fully understood by
   those who wield those tools and by those who make used of results
   obtained with those tools. When a scientific tool exists as software,
   access to source code is an important element in achieving full
   understanding of that tool. As our field evolves and new versions of
   software are required, access to source allows us to adapt our tools
   quickly and effectively.

   In the early days of software development, most scientific software
   source code was freely and openly shared with a minimum of formalities.
   These days, it appears that carefully drawn legal documents are
   necessary to protect free access to the source code of scientific
   software. We are all deeply indebted to [13]Richard Stallman for
   showing us how a creative combination of copyrights and seemingly
   restrictive licenses could give us truly unfettered freedom to use
   programs, to read their source code and to develop new versions. The
   [14]GNU project, and the [15]Linux project have shown that an open
   source approach works. We use the GNU General Public License (the
   [16]"GPL") for our programs starting with the release of CIFtbx3. Older
   versions use the license from [17]OpenRasmol. The OpenRasMol conditions
   for use have correctly been called "GPL-like".

   If you are a user of these programs, you will find that the copyrights
   and notices ask little more of you than that you avoid mistakes by
   others by keeping the notices with copies, display scientific integrity
   by citing your sources properly and treating this like other shared
   scientific developments by not inferring a warranty. If you are a
   software developer and wish to incorporate what you find here into new
   code, or to pick up bits and pieces and use them in another context,
   the situation becomes more complex. Read the notices carefully. You
   will find that they are "infectious". Whatever you make from our Open
   Source code must itself be offered as Open Source code. In addition, in
   order to allow users to understand what has changed and to ensure
   orderly development you have to describe your changes.
     __________________________________________________________________

   [18]CIFtbx Primer Plus (320K in PDF format) provides documentation on
   CIFtbx.
     __________________________________________________________________

   In order to get a complete release of CIFtbx4, CYCLOPS2, cif2cif,
   cif2xml you will need either a C-shell archive or a shell archive of
   each package. That is, you need either

   [19]ciftbx.cshar.Z, [20]cyclops.cshar.Z, [21]cif2cif.cshar.Z,
   [22]cif2xml.cshar.Z and [23]cif2pdb.cshar.Z or

   [24]ciftbx.shar.Z, [25]cyclops.shar.Z, [26]cif2cif.shar.Z,
   [27]cif2xml.shar.Z and [28]cif2pdb.shar.Z

   You do not need both sets. If you cannot decompress files at your end,
   then you may wish to have [29]ciftbx.cshar, [30]cyclops.cshar,
   [31]cif2cif.cshar, [32]cif2xml.cshar and [33]cif2pdb.cshar

   In order to test the programs, you will need at least the following CIF
   dictionaries: [34]cif_core.dic.Z [35]cif_mm.dic.Z and
   [36]cif_mm_pdbx.dic.Z Check the IUCr web page at
   [37]http://www.iucr.org for latest versions.

   The directory structure within which you will work is

                                 top level directory
                                 -------------------
                                         |
                                         |
     --------------------------------------------------------------------------
     |              |             |              |              |             |
[38]dictionaries   [39]ciftbx.src     [40]cyclops.src   [41]cif2cif.src   [42]ci
f2xml.src   [43]cif2pdb.src
------------   ----------     -----------   -----------   -----------   --------
---

   In order to save space and transmission time, it is possible that each
   archive will be compressed before you pick it up. Place the archives in
   the top level directory and the dictionaries into the 'dictionaries'
   directory. Be sure to uncompress the archives before trying to unpack
   them. If you are on a UNIX system, leave the dictionaries compressed.

   Each archive contains a detailed README file for the package involved.
   Please do read the README. The general approach is:

   1. unpack the archive

   2. make all

   3. make tests

   Since all this code depends on CIFtbx, you must install CIFtbx before
   installing CYCLOPS2, cif2cif, cif2xml or cif2pdb. If you don't need
   CYCLOPS2 or cif2cif or cif2xml or cif2pdb, you may leave them out, but
   they are good examples of working CIFtbx applications, so we suggest
   taking a look at them if you are new to CIFtbx.
     __________________________________________________________________


    For further information contact Syd Hall ( syd@crystal.uwa.edu.au )
    or Herbert Bernstein ( yayahjb@gmail.com )
     __________________________________________________________________

        The CIFtbx site is provided courtesy of [44]Bernstein + Sons,
                      Information Systems Consultants.

   Portions © Copyright Herbert J. Bernstein 2000, 2005, 2009, 2024. All
   Rights Reserved. Other copyrights apply. License to copy most pages on
   this site will be granted if certain open source and other conditions
   are adhered to. See
   [45]http://www.bernstein-plus-sons.com/software/ciftbx_4.1.0/NOTICE.htm
   l. To request permission to copy any elements from our pages, or to
   send comments about our pages, please write to
   [46]webmaster@bernstein-plus-sons.co m. If you establish a link to one
   of our pages, please let us know! Updated 14 August 2024

References

   1. http://www.iucr.org/iucr-top/welcome.html
   2. http://www.iucr.org/iucr-top/cif/home.html
   3. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/ciftbx.src/README.ciftbx.html
   4. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cyclops.src/README.cyclops.html
   5. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cif2cif.src/README.cif2cif.html
   6. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cif2xml.src/README.cif2xml.html
   7. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cif2pdb.src/README.cif2pdb.html
   8. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/gpl.txt
   9. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/lgpl.txt
  10. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/NOTICE.html
  11. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/IUCR_POLICY.html
  12. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/NOTICE.html
  13. http://www.stallman.org/
  14. http://www.gnu.org/
  15. http://www.linux.org/
  16. http://www.gnu.org/copyleft/gpl.html
  17. http://www.openrasmol.org/
  18. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/CIFtbx_Primer.pdf
  19. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/ciftbx.cshar.Z
  20. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cyclops.cshar.Z
  21. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cif2cif.cshar.Z
  22. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cif2xml.cshar.Z
  23. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cif2pdb.cshar.Z
  24. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/ciftbx.shar.Z
  25. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cyclops.shar.Z
  26. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cif2cif.shar.Z
  27. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cif2xml.shar.Z
  28. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cif2pdb.shar.Z
  29. file:///cgi-bin/yaya/decomp.cgi/NDB/mmcif/software/ciftbx_4.1.0/ciftbx.cshar
  30. file:///cgi-bin/yaya/decomp.cgi/NDB/mmcif/software/ciftbx_4.1.0/cyclops.cshar
  31. file:///cgi-bin/yaya/decomp.cgi/NDB/mmcif/software/ciftbx_4.1.0/cif2cif.cshar
  32. file:///cgi-bin/yaya/decomp.cgi/NDB/mmcif/software/ciftbx_4.1.0/cif2xml.cshar
  33. file:///cgi-bin/yaya/decomp.cgi/NDB/mmcif/software/ciftbx_4.1.0/cif2pdb.cshar
  34. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/dictionaries/cif_core.dic.Z
  35. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/dictionaries/cif_mm.dic.Z
  36. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/dictionaries/cif_mm_pdbx.dic.Z
  37. http://www.iucr.org/
  38. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/dictionaries
  39. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/ciftbx.src
  40. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cyclops.src
  41. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cif2cif.src
  42. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cif2xml.src
  43. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cif2pdb.src
  44. http://www.bernstein-plus-sons.com/
  45. http://www.bernstein-plus-sons.com/software/ciftbx_4.1.0/NOTICE.html
  46. mailto:webmaster@bernstein-plus-sons.com